RNA interference (RNAi) is a phenomenon wherein double-stranded RNA (dsRNA), when present in a cell, inhibits expression of a gene that has a sufficiently complementary sequence to a single strand in the double-stranded RNA. Inhibition of gene expression is caused by degradation of messenger RNA (mRNA) transcribed from the target gene [Sharp et al., Genes and Development 15: 485-490 (2001)]. The double-stranded RNA responsible for inducing RNAi is termed interfering RNA. The mechanism and cellular machinery through which dsRNA mediates RNAi has been investigated using both genetic and biochemical approaches. Biochemical analyses suggest that dsRNA introduced into the cytoplasm of a cell is first processed into RNA fragments 21-25 nucleotides long [Hammond et al., Nature 404: 293-296 (2000); Hamilton et al., Science 286: 950-952 (1999); Zamore et al., Cell 101: 25-33 (2000); Yang et al., Current Biology 10: 1191-1200 (2000); Parrish et al., Molecular Cell 6: 1077-1087 (2000)]. It has been shown in in vitro studies that these dsRNAs, termed small interfering RNAs (siRNA) are generated at least in one mechanism by the RNAse III-like enzyme Dicer [Hammond et al., Nature 404: 293-296 (2000)]. These siRNAs likely act as guides for mRNA cleavage, as the target mRNA is cleaved at a position in the center of the region hybridized to a particular siRNA [Sharp 2001]. Biochemical evidence suggests that the siRNA is part of a multicomponent nuclease complex termed the RNA-induced silencing complex (RISC) [Hammond et al., Nature 404: 293-296 (2000)]. One of the proteins of this complex, Argonaute2, has been identified as a product of the argonaute gene family [Sharp et al., Genes and Development 15: 485-490 (2001);]. This protein is essential for mouse development, and cells lacking Argonaute2 are unable to mount an experimental response to siRNAs. Mutations within a cryptic ribonuclease H domain within Argonaute2, as identified by comparison with the structure of an archeal Argonaute protein, inactivate RISC. Thus, Argonaute contributes “Slicer” activity to RISC, providing the catalytic engine for RNAi [Liu et al., Science 305(5689): 1437-1441 (2004)].
This gene family, which also contains the C. elegans homolog rde-1 and related genes, the N. crassa homolog qde-2, and the Arabidopsis homolog arg-1, has been shown to be required for RNAi through genetic studies [Sharp et al., Genes and Development 15: 485-490 (2001); Hammond et al., Nature 404: 293-296 (2000); Hamilton et al., Science 286: 950-952 (1999)]. Genetic screens in C. elegans have also identified the mut-7 gene as essential for RNAi. This gene bears resemblance to RNAse D, suggesting that its gene product acts in the mRNA degradation step of the reaction [Sharp et al., Genes and Development 15: 485-490 (2001)].
Over the past decade, researchers have designed, synthesized, studied, and applied polyvalent DNA-functionalized gold nanoparticles (DNA-Au NPs). [Mirkin et al., Nature 382: 607 (1996)]. These efforts have resulted in a new fundamental understanding of hybrid nanostructures [Demers et al., Anal. Chem. 72: 5535 (2000); Jin et al., J. Am. Chem. Soc. 125: 1643 (2003); Lytton-Jean et al., J. Am. Chem Soc 127: 12754-12754 (2005); Storhoff et al., J. Am. Chem. Soc. 122: 4640 (2000); You et al., Soft Matter 2: 190 (2006); Wang et al., Nanomed. 1: 413 (2006)], important and in certain cases commercially viable detection and diagnostic assays [Nam et al., Science 301: 1884 (2003); Stoeva et al., J. Am. Chem. Soc. 128: 8378 (2006); Liu et al., J. Am. Chem. Soc. 126: 12298 (2004); Faulds et al., Anal. Chem. 76: 412 (2004)], and the ability to program materials assembly through the use of DNA synthons [Mirkin et al., Nature 382: 607 (1996); Park et al., Nature 451: 553 (2008); Nykypanchuk et al., Nature, 451: 549 (2008)]. Polyvalent DNA-Au NPs have several unique properties, such as sharp and elevated melting temperatures [Jin et al., J. Am. Chem. Soc. 125: 1643 (2003)], enhanced binding properties [Lytton-Jean et al., J. Am. Chem Soc 127: 12754-12754 (2005)] (as compared with free strands of the same sequence) and distance-dependent optical properties [Elghanian et al., Science 277: 1078 (1997)]. In agreement with research on polyvalent molecular systems [Gestwicki et al., J. Am. Chem. Soc. 124: 14922 (2002)], the high surface DNA density and the ability of the nanoparticles to engage in multidentate interactions are the proposed origin of these unique properties.